Add transform interface and default op

Author: bnorthan

src/main/java/net/imagej/ops/transform/TransformNamespace.java

@@ -50,7 +50,7 @@
 import net.imglib2.img.array.ArrayImg;
 import net.imglib2.interpolation.InterpolatorFactory;
 import net.imglib2.outofbounds.OutOfBoundsFactory;
-import net.imglib2.realtransform.RealTransform;
+import net.imglib2.realtransform.InvertibleRealTransform;
 import net.imglib2.transform.integer.shear.InverseShearTransform;
 import net.imglib2.transform.integer.shear.ShearTransform;
 import net.imglib2.type.Type;
@@ -1207,4 +1207,59 @@ public <T extends Type<T>> RandomAccessibleInterval<T> concatenateView(
 			ConcatenateViewWithAccessMode.class, source, concatenationAxis, mode);
 	}
 
+	@OpMethod(
+		op = net.imagej.ops.transform.realTransform.DefaultTransformView.class)
+	public <T extends RealType<T>> RandomAccessibleInterval<T> realTransform(
+		final RandomAccessibleInterval<T> in,
+		final InvertibleRealTransform transform)
+	{
+		final RandomAccessibleInterval<T> result =
+			(RandomAccessibleInterval<T>) ops().run(
+				net.imagej.ops.transform.realTransform.DefaultTransformView.class, in,
+				transform);
+		return result;
+	}
+
+	@OpMethod(
+		op = net.imagej.ops.transform.realTransform.DefaultTransformView.class)
+	public <T extends RealType<T>> RandomAccessibleInterval<T> realTransform(
+		final RandomAccessibleInterval<T> in,
+		final InvertibleRealTransform transform, final Interval outputInterval)
+	{
+		final RandomAccessibleInterval<T> result =
+			(RandomAccessibleInterval<T>) ops().run(
+				net.imagej.ops.transform.realTransform.DefaultTransformView.class, in,
+				transform, outputInterval);
+		return result;
+	}
+
+	@OpMethod(
+		op = net.imagej.ops.transform.realTransform.DefaultTransformView.class)
+	public <T extends RealType<T>> RandomAccessibleInterval<T> realTransform(
+		final RandomAccessibleInterval<T> in,
+		final InvertibleRealTransform transform, final Interval outputInterval,
+		final InterpolatorFactory<T, RandomAccessible<T>> interpolator)
+	{
+		final RandomAccessibleInterval<T> result =
+			(RandomAccessibleInterval<T>) ops().run(
+				net.imagej.ops.transform.realTransform.DefaultTransformView.class, in,
+				transform, outputInterval, interpolator);
+		return result;
+	}
+
+	@OpMethod(
+		op = net.imagej.ops.transform.realTransform.DefaultTransformView.class)
+	public <T extends RealType<T>> RandomAccessibleInterval<T> realTransform(
+		final RandomAccessibleInterval<T> in,
+		final InvertibleRealTransform transform, final Interval outputInterval,
+		final InterpolatorFactory<T, RandomAccessible<T>> interpolator,
+		final OutOfBoundsFactory<T, RandomAccessibleInterval<T>> outOfBoundsFactory)
+	{
+		final RandomAccessibleInterval<T> result =
+			(RandomAccessibleInterval<T>) ops().run(
+				net.imagej.ops.transform.realTransform.DefaultTransformView.class, in,
+				transform, outputInterval, interpolator, outOfBoundsFactory);
+		return result;
+	}
+
 }

src/main/java/net/imagej/ops/transform/realTransform/DefaultTransformView.java

@@ -0,0 +1,103 @@
+/*
+ * #%L
+ * ImageJ software for multidimensional image processing and analysis.
+ * %%
+ * Copyright (C) 2014 - 2018 ImageJ developers.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package net.imagej.ops.transform.realTransform;
+
+import net.imagej.ops.Ops;
+import net.imagej.ops.special.function.AbstractUnaryFunctionOp;
+import net.imglib2.FinalInterval;
+import net.imglib2.Interval;
+import net.imglib2.RandomAccessible;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.interpolation.InterpolatorFactory;
+import net.imglib2.interpolation.randomaccess.LanczosInterpolatorFactory;
+import net.imglib2.outofbounds.OutOfBoundsFactory;
+import net.imglib2.outofbounds.OutOfBoundsMirrorFactory;
+import net.imglib2.realtransform.InvertibleRealTransform;
+import net.imglib2.realtransform.RealViews;
+import net.imglib2.type.numeric.NumericType;
+import net.imglib2.type.numeric.RealType;
+import net.imglib2.view.IntervalView;
+import net.imglib2.view.Views;
+
+import org.scijava.Priority;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+/**
+ * Applies an Affine transform to a {@link RandomAccessibleInterval}
+ *
+ * @author Brian Northan (True North Intelligent Algorithms)
+ * @author Martin Horn (University of Konstanz)
+ * @author Stefan Helfrich (University of Konstanz)
+ */
+@Plugin(type = Ops.Transform.RealTransform.class, priority = Priority.HIGH + 1)
+public class DefaultTransformView<T extends NumericType<T> & RealType<T>>
+	extends
+	AbstractUnaryFunctionOp<RandomAccessibleInterval<T>, RandomAccessibleInterval<T>>
+	implements Ops.Transform.RealTransform
+{
+
+	/**
+	 * The transform to apply
+	 */
+	@Parameter
+	InvertibleRealTransform transform;
+
+	@Parameter(required = false)
+	private Interval outputInterval = null;
+
+	@Parameter(required = false)
+	private InterpolatorFactory<T, RandomAccessible<T>> interpolator = null;
+
+	@Parameter(required = false)
+	private OutOfBoundsFactory<T, RandomAccessibleInterval<T>> outOfBoundsFactory =
+		new OutOfBoundsMirrorFactory<>(OutOfBoundsMirrorFactory.Boundary.SINGLE);
+
+	@Override
+	public RandomAccessibleInterval<T> calculate(
+		final RandomAccessibleInterval<T> input)
+	{
+
+		if (outputInterval == null) {
+			outputInterval = new FinalInterval(input);
+		}
+
+		if (interpolator == null) {
+			interpolator = new LanczosInterpolatorFactory<>();
+		}
+
+		final IntervalView<T> interval = Views.interval(Views.raster(RealViews
+			.transformReal(Views.interpolate(Views.extendZero(input), interpolator),
+				transform)), outputInterval);
+
+		return interval;
+	}
+
+}

src/main/templates/net/imagej/ops/Ops.list

@@ -448,6 +448,7 @@ namespaces = ```
 		[name: "translateView",                  iface: "TranslateView"],
 		[name: "unshearView",                    iface: "UnshearView"],
 		[name: "zeroMinView",                    iface: "ZeroMinView"],
+		[name: "realTransform",                  iface: "RealTransform"],
 	]],
 	[name: "zernike", iface: "Zernike", ops: [
 		[name: "magnitude",                      iface: "Magnitude"],